import math
import os
import netCDF4 as nc
import numpy as np
import xarray as xr
from mpas_tools.io import write_netcdf
from mpas_tools.viz.paraview_extractor import extract_vtk
from shapely.geometry import Point
from shapely.geometry.polygon import Polygon
from compass.step import Step
[docs]
class LTSRegionsStep(Step):
"""
A step for adding LTS regions to a global MPAS-Ocean mesh
Attributes
----------
cull_mesh_step : compass.ocean.mesh.cull.CullMeshStep
The culled mesh step containing input files to this step
"""
[docs]
def __init__(self, test_case, cull_mesh_step,
name='lts_regions', subdir='lts_regions'):
"""
Create a new step
Parameters
----------
test_case : compass.Testcase
The test case this step belongs to
cull_mesh_step : compass.ocean.mesh.cull.CullMeshStep
The culled mesh step containing input files to this step
name : str, optional
the name of the step
subdir : str, optional
the subdirectory for the step. The default is ``name``
"""
super().__init__(test_case, name=name, subdir=subdir)
for file in ['lts_mesh.nc', 'lts_graph.info']:
self.add_output_file(filename=file)
self.cull_mesh_step = cull_mesh_step
[docs]
def setup(self):
"""
Set up the test case in the work directory, including downloading any
dependencies.
"""
super().setup()
self.lts_fine_regions_file = 'hurricane_lts_fine_regions.nc'
self.add_input_file(
filename=self.lts_fine_regions_file,
target=self.lts_fine_regions_file,
database='hurricane')
cull_path = self.cull_mesh_step.path
tgt1 = os.path.join(cull_path, 'culled_mesh.nc')
self.add_input_file(filename='culled_mesh.nc', work_dir_target=tgt1)
tgt2 = os.path.join(cull_path, 'culled_graph.info')
self.add_input_file(filename='culled_graph.info', work_dir_target=tgt2)
[docs]
def run(self):
"""
Run this step of the test case
"""
file_name = self.lts_fine_regions_file
fine_rgn = nc.Dataset(file_name, 'r', format='NETCDF4_64BIT')
region = 'east_us_coast'
if region == 'east_us_coast':
east_us_coast = fine_rgn.variables['east_us_coast_pts'][:, :]
fine_region = Polygon(east_us_coast)
elif region == 'western_atlantic':
western_atlantic = fine_rgn.variables['western_atlantic_pts'][:, :]
fine_region = Polygon(western_atlantic)
elif region == 'delaware_coast':
delaware_coast = fine_rgn.variables['delaware_coast_pts'][:, :]
fine_region = Polygon(delaware_coast)
use_progress_bar = self.log_filename is None
label_mesh(fine_region, mesh='culled_mesh.nc',
graph_info='culled_graph.info', num_interface=2,
logger=self.logger, use_progress_bar=use_progress_bar)
[docs]
def label_mesh(fine_region, mesh, graph_info, num_interface, # noqa: C901
logger, use_progress_bar):
# read in mesh data
ds = xr.open_dataset(mesh)
n_cells = ds['nCells'].size
n_edges = ds['nEdges'].size
area_cell = ds['areaCell'].values
cells_on_edge = ds['cellsOnEdge'].values
edges_on_cell = ds['edgesOnCell'].values
lat_cell = ds['latCell']
lon_cell = ds['lonCell']
# start by setting all cells to coarse
lts_rgn = [2] * n_cells
# check each cell, if in the fine region, label as fine
logger.info('Labeling fine cells...')
for icell in range(0, n_cells):
cell_pt = Point(lat_cell[icell], lon_cell[icell])
if fine_region.contains(cell_pt):
lts_rgn[icell] = 1
# first layer of cells with label 5
changed_cells = [[], []]
for iedge in range(0, n_edges):
cell1 = cells_on_edge[iedge, 0] - 1
cell2 = cells_on_edge[iedge, 1] - 1
if (cell1 != -1 and cell2 != -1):
if (lts_rgn[cell1] == 1 and lts_rgn[cell2] == 2):
lts_rgn[cell2] = 5
changed_cells[0].append(cell2)
elif (lts_rgn[cell1] == 2 and lts_rgn[cell2] == 1):
lts_rgn[cell1] = 5
changed_cells[0].append(cell1)
# second and third layer of cells with label 5
# only looping over cells changed during loop for previous layer
# at the end of this loop, changed_cells[0] will have the list of cells
# sharing edegs with the coarse cells
logger.info('Labeling interface-adjacent fine cells...')
for i in range(0, 2): # this loop creates 2 layers
changed_cells[(i + 1) % 2] = []
for icell in changed_cells[i % 2]:
edges = edges_on_cell[icell]
for iedge in edges:
if iedge != 0:
cell1 = cells_on_edge[iedge - 1, 0] - 1
cell2 = cells_on_edge[iedge - 1, 1] - 1
if (cell1 != -1 and cell2 != -1):
if (lts_rgn[cell1] == 5 and lts_rgn[cell2] == 2):
lts_rgn[cell2] = 5
changed_cells[(i + 1) % 2].append(cell2)
elif (lts_rgn[cell1] == 2 and lts_rgn[cell2] == 5):
lts_rgn[cell1] = 5
changed_cells[(i + 1) % 2].append(cell1)
# n layers of interface region with label 4
logger.info('Labeling interface cells...')
for i in range(0, num_interface):
changed_cells[(i + 1) % 2] = []
for icell in changed_cells[i % 2]:
edges = edges_on_cell[icell]
for iedge in edges:
if iedge != 0:
cell1 = cells_on_edge[iedge - 1, 0] - 1
cell2 = cells_on_edge[iedge - 1, 1] - 1
if (cell1 != -1 and cell2 != -1):
# for the first layer, need to check neighbors are
# 5 and 2
# for further layers, need to check neighbors are
# 3 and 2
if (i == 0):
if (lts_rgn[cell1] == 5 and lts_rgn[cell2] == 2):
lts_rgn[cell2] = 3
changed_cells[(i + 1) % 2].append(cell2)
elif (lts_rgn[cell1] == 2 and lts_rgn[cell2] == 5):
lts_rgn[cell1] = 3
changed_cells[(i + 1) % 2].append(cell1)
else:
if (lts_rgn[cell1] == 3 and lts_rgn[cell2] == 2):
lts_rgn[cell2] = 3
changed_cells[(i + 1) % 2].append(cell2)
elif (lts_rgn[cell1] == 2 and lts_rgn[cell2] == 3):
lts_rgn[cell1] = 3
changed_cells[(i + 1) % 2].append(cell1)
changed_cells[0] = changed_cells[num_interface % 2]
# n layers of interface region with label 3
for i in range(0, num_interface):
changed_cells[(i + 1) % 2] = []
for icell in changed_cells[i % 2]:
edges = edges_on_cell[icell]
for iedge in edges:
if iedge != 0:
cell1 = cells_on_edge[iedge - 1, 0] - 1
cell2 = cells_on_edge[iedge - 1, 1] - 1
if (cell1 != -1 and cell2 != -1):
# for the first layer, need to check neighbors are
# 5 and 2
# for further layers, need to check neighbors are
# 3 and 2
if (i == 0):
if (lts_rgn[cell1] == 3 and lts_rgn[cell2] == 2):
lts_rgn[cell2] = 4
changed_cells[(i + 1) % 2].append(cell2)
elif (lts_rgn[cell1] == 2 and lts_rgn[cell2] == 3):
lts_rgn[cell1] = 4
changed_cells[(i + 1) % 2].append(cell1)
else:
if (lts_rgn[cell1] == 4 and lts_rgn[cell2] == 2):
lts_rgn[cell2] = 4
changed_cells[(i + 1) % 2].append(cell2)
elif (lts_rgn[cell1] == 2 and lts_rgn[cell2] == 4):
lts_rgn[cell1] = 4
changed_cells[(i + 1) % 2].append(cell1)
# create lts_mesh.nc
logger.info('Creating lts_mesh...')
# open mesh nc file to be copied
ds_msh = xr.open_dataset(mesh)
ds_ltsmsh = ds_msh.copy(deep=True)
ltsmsh_name = 'lts_mesh.nc'
write_netcdf(ds_ltsmsh, ltsmsh_name)
mshnc = nc.Dataset(ltsmsh_name, 'a', format='NETCDF4_64BIT_OFFSET')
try:
# try to get LTSRegion and assign new value
lts_rgn_NC = mshnc.variables['LTSRegion']
lts_rgn_NC[:] = lts_rgn[:]
except KeyError:
# create new variable
ncells_NC = mshnc.dimensions['nCells'].name
lts_rgns_NC = mshnc.createVariable('LTSRegion', np.int32, (ncells_NC,))
# set new variable
lts_rgns_NC[:] = lts_rgn[:]
mshnc.close()
extract_vtk(ignore_time=True, lonlat=0,
dimension_list=['maxEdges='],
variable_list=['allOnCells'],
filename_pattern=ltsmsh_name,
out_dir='lts_mesh_vtk', use_progress_bar=use_progress_bar)
# label cells in graph.info
logger.info('Weighting ' + graph_info + '...')
fine_cells = 0
coarse_cells = 0
newf = ""
with open(graph_info, 'r') as f:
lines = f.readlines()
# this is to have fine, coarse and interface be separate for METIS
# newf += lines[0].strip() + " 010 3 \n"
# this is to have fine, and interface be together for METIS
newf += lines[0].strip() + " 010 2 \n"
for icell in range(1, len(lines)):
if (lts_rgn[icell - 1] == 1 or lts_rgn[icell - 1] == 5): # fine
# newf+= "0 1 0 " + lines[icell].strip() + "\n"
newf += "0 1 " + lines[icell].strip() + "\n"
fine_cells = fine_cells + 1
elif (lts_rgn[icell - 1] == 2): # coarse
# newf+= "1 0 0 " + lines[icell].strip() + "\n"
newf += "1 0 " + lines[icell].strip() + "\n"
coarse_cells = coarse_cells + 1
else: # interface 1 and 2
# newf+= "0 0 1 " + lines[icell].strip() + "\n"
newf += "0 1 " + lines[icell].strip() + "\n"
coarse_cells = coarse_cells + 1
with open('lts_graph.info', 'w') as f:
f.write(newf)
max_area = max(area_cell)
min_area = min(area_cell)
max_width = 2 * np.sqrt(max_area / math.pi) / 1000
min_width = 2 * np.sqrt(min_area / math.pi) / 1000
area_ratio = max_area / min_area
width_ratio = max_width / min_width
number_ratio = coarse_cells / fine_cells
txt = 'number of fine cells = {}\n'.format(fine_cells)
txt += 'number of coarse cells = {}\n'.format(coarse_cells)
txt += 'ratio of coarse to fine cells = {}\n'.format(number_ratio)
txt += 'ratio of largest to smallest cell area = {}\n'.format(area_ratio)
txt += 'ratio of largest to smallest cell width = {}\n'.format(width_ratio)
txt += 'number of interface layers = {}\n'.format(num_interface)
logger.info(txt)
with open('lts_mesh_info.txt', 'w') as f:
f.write(txt)